1# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- 2# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 3# 4# MDAnalysis --- https://www.mdanalysis.org 5# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors 6# (see the file AUTHORS for the full list of names) 7# 8# Released under the GNU Public Licence, v2 or any higher version 9# 10# Please cite your use of MDAnalysis in published work: 11# 12# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, 13# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. 14# MDAnalysis: A Python package for the rapid analysis of molecular dynamics 15# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th 16# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. 17# 18# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. 19# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. 20# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 21# 22from __future__ import absolute_import 23 24import MDAnalysis as mda 25from MDAnalysisTests.datafiles import PDBQT_input, PDBQT_querypdb 26from MDAnalysis.lib.NeighborSearch import AtomNeighborSearch 27 28from numpy.testing import ( 29 assert_equal, 30) 31import pytest 32 33from MDAnalysisTests import make_Universe 34 35 36class TestPDBQT(object): 37 @pytest.fixture() 38 def universe(self): 39 """Set up the standard AdK system in implicit solvent.""" 40 return mda.Universe(PDBQT_input) 41 42 def test_segid(self, universe): 43 sel = universe.select_atoms('segid A') 44 assert_equal(sel.n_atoms, 909, "failed to select segment A") 45 sel = universe.select_atoms('segid B') 46 assert_equal(sel.n_atoms, 896, "failed to select segment B") 47 48 def test_protein(self, universe): 49 sel = universe.select_atoms('protein') 50 assert_equal(sel.n_atoms, 1805, "failed to select protein") 51 assert_equal(sel.atoms.ix, universe.atoms.ix, 52 "selected protein is not the same as auto-generated protein segment A+B") 53 54 def test_backbone(self, universe): 55 sel = universe.select_atoms('backbone') 56 assert_equal(sel.n_atoms, 796) 57 58 def test_neighborhood(self, universe): 59 '''test KDTree-based distance search around query atoms 60 61 Creates a KDTree of the protein and uses the coordinates of 62 the atoms in the query pdb to create a list of protein 63 residues within 4.0A of the query atoms. 64 ''' 65 query_universe = mda.Universe(PDBQT_querypdb) # PDB file 66 67 protein = universe.select_atoms("protein") 68 ns_protein = AtomNeighborSearch(protein) 69 query_atoms = query_universe.atoms 70 residue_neighbors = ns_protein.search(query_atoms, 4.0) 71 assert_equal(len(residue_neighbors), 80) 72 73 def test_n_frames(self, universe): 74 assert_equal(universe.trajectory.n_frames, 1, 75 "wrong number of frames in pdb") 76 77 def test_time(self, universe): 78 assert_equal(universe.trajectory.time, 0.0, "wrong time of the frame") 79 80 def test_frame(self, universe): 81 assert_equal(universe.trajectory.frame, 0, 82 "wrong frame number (0-based, should be 0 for single frame readers)") 83 84 85class TestPDBQTWriter(object): 86 reqd_attributes = ['names', 'types', 'resids', 'resnames', 'radii', 87 'charges'] 88 89 @pytest.fixture() 90 def outfile(self, tmpdir): 91 return str(tmpdir) + 'out.pdbqt' 92 93 def test_roundtrip_writing_coords(self, outfile): 94 u = mda.Universe(PDBQT_input) 95 u.atoms.write(outfile) 96 u2 = mda.Universe(outfile) 97 98 assert_equal(u2.atoms.positions, u.atoms.positions, 99 "Round trip does not preserve coordinates") 100 101 def test_roundtrip_formatting(self, outfile): 102 # Compare formatting of first line 103 u = mda.Universe(PDBQT_input) 104 u.atoms.write(outfile) 105 106 with open(PDBQT_input, 'r') as inf: 107 l_ref = inf.readline().strip() 108 with open(outfile, 'r') as inf: 109 inf.readline() # header 110 inf.readline() # cryst 111 l_new = inf.readline().strip() 112 assert l_ref == l_new 113 114 @staticmethod 115 def assert_writing_warns(u, outfile): 116 with pytest.warns(UserWarning): 117 u.atoms.write(outfile) 118 119 def test_write_no_charges(self, outfile): 120 attrs = self.reqd_attributes 121 attrs.remove('charges') 122 u = make_Universe(attrs, trajectory=True) 123 124 self.assert_writing_warns(u, outfile) 125 126 u2 = mda.Universe(outfile) 127 128 assert all(u2.atoms.charges == 0.0) 129 130 def test_write_no_chainids_with_segids(self, outfile): 131 attrs = self.reqd_attributes 132 attrs.append('segids') 133 u = make_Universe(attrs, trajectory=True) 134 135 u.atoms.write(outfile) 136 u2 = mda.Universe(outfile) 137 138 # Should have used last letter of segid as chainid 139 assert all(u2.atoms[:25].segids == 'A') 140 assert all(u2.atoms[25:50].segids == 'B') 141 142 def test_get_writer(self, outfile): 143 u = mda.Universe(PDBQT_input) 144 w = u.trajectory.Writer(outfile) 145 146 assert isinstance(w, mda.coordinates.PDBQT.PDBQTWriter) 147 w.close() 148